Contacts of the helix formed by residues 119 - 133 (chain B) in PDB entry 5HRI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ARG* 3.6 36.6 - - - +
117B THR 3.7 0.4 - - - -
118B GLY* 1.3 89.0 - - - +
120B VAL* 1.3 66.8 + - - +
121B SER* 4.2 12.6 - - - +
122B TYR* 3.2 24.2 + - + +
123B LEU* 3.2 9.4 + - - +
173B ARG 3.3 29.6 - - - +
174B LEU* 4.7 6.7 - - + -
201B DGT 4.4 2.0 - - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLY* 4.1 0.2 - - - -
119B PRO* 1.3 73.9 - - - +
121B SER* 1.3 64.7 + - - +
123B LEU* 3.0 11.1 + - - +
124B ILE* 3.0 41.8 + - + +
201B DGT 3.4 66.3 + - + +
9F C 4.2 2.5 - - - +
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO* 4.2 11.9 - - - +
120B VAL* 1.3 81.2 - - - +
122B TYR* 1.3 63.2 + - - +
124B ILE* 3.5 11.6 + - - +
125B ARG* 3.3 24.1 + - - +
174B LEU* 4.3 18.0 + - - +
8F T 5.9 1.4 - - - -
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 3.6 38.2 - + - -
118B GLY 3.8 16.8 - - - -
119B PRO* 3.2 21.9 + - + +
120B VAL 3.2 0.2 - - - -
121B SER* 1.3 79.9 + - - +
123B LEU* 1.3 70.5 + - + +
125B ARG* 3.3 24.8 - - - +
126B ILE* 3.1 51.2 + - + +
160B ILE* 4.7 6.8 - - - +
165B PHE* 4.9 1.6 - - - +
166B THR 4.2 13.7 + - - -
168B ARG* 4.6 5.6 + - - +
173B ARG* 3.8 22.4 - - + +
174B LEU* 3.6 36.6 - - - +
1H A 4.5 3.1 - - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 3.7 34.3 - - + +
115B HIS* 3.1 29.4 - - - +
118B GLY* 4.0 12.3 - - - -
119B PRO 3.4 10.3 - - - +
120B VAL* 3.0 7.3 + - - +
122B TYR* 1.3 86.5 - - + +
124B ILE* 1.3 59.9 + - + +
126B ILE* 3.4 4.3 + - + +
127B ARG* 2.9 49.4 + - - +
137B LEU* 6.4 0.2 - - + -
201B DGT 3.5 42.0 - - + +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B VAL* 3.0 30.9 + - + +
121B SER* 3.7 12.1 - - - +
123B LEU* 1.3 77.2 - - + +
125B ARG* 1.3 59.3 + - - +
128B ALA* 2.9 27.9 + - - +
8F T 3.8 41.5 - - + -
9F C 3.7 55.1 - - + +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER 3.3 11.5 + - - +
122B TYR* 3.3 24.3 - - - +
124B ILE* 1.3 77.1 - - - +
126B ILE* 1.3 77.9 + - - +
128B ALA* 3.9 1.4 - - - +
129B ALA* 3.2 23.6 + - - +
165B PHE* 5.0 0.2 - - - -
168B ARG* 3.7 4.4 - - - +
174B LEU* 2.9 39.1 + - - -
8F T 4.1 16.6 - - + +
1H A 2.8 112.5 + - + +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 4.3 20.4 - - + -
122B TYR* 3.1 56.7 + - + +
123B LEU* 3.7 5.8 - - - +
125B ARG* 1.3 86.8 - - + +
127B ARG* 1.3 63.6 + - + +
129B ALA* 3.4 3.8 + - - +
130B LEU* 3.2 32.4 + - + +
137B LEU* 4.4 4.7 - - + -
163B LEU* 5.3 0.4 - - + -
165B PHE* 3.5 53.0 - - + -
1H A 4.7 0.7 - - - -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 6.3 0.8 - - - -
115B HIS* 3.1 33.3 + - - +
123B LEU* 2.9 31.6 + - - +
126B ILE* 1.3 74.9 - - + +
128B ALA* 1.3 60.4 + - - +
130B LEU* 3.4 7.3 + - - +
131B LYS* 2.9 29.3 + - - +
135B TYR 5.0 0.5 - - - +
137B LEU* 3.4 41.2 + - + +
138B ASN* 3.6 23.4 + - - +
139B GLN* 5.1 0.8 + - - -
201B DGT 3.2 13.8 + - - -
9F C 3.0 52.4 + - - +
10F T 3.1 26.5 + - - +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ILE 2.9 17.9 + - - +
125B ARG 3.9 3.1 - - - +
126B ILE 3.3 0.2 - - - -
127B ARG* 1.3 75.6 - - - +
129B ALA* 1.3 63.7 + - - +
131B LYS* 3.3 7.9 + - - +
132B LYS* 3.1 34.5 + - - +
8F T 3.6 29.8 - - - +
9F C 3.8 20.1 - - - +
1H A 5.9 0.2 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ARG 3.2 15.6 + - - +
126B ILE 3.7 5.2 - - - +
127B ARG 3.3 0.2 - - - -
128B ALA* 1.3 80.8 - - - +
130B LEU* 1.3 61.1 + - - +
132B LYS* 3.4 21.9 + - - +
133B LYS* 3.6 15.6 + - - +
165B PHE* 4.0 20.0 - - + -
1H A 5.3 11.2 - - - +
2H T 5.5 11.2 - - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE* 3.2 23.1 + - + +
127B ARG* 3.8 5.2 - - - +
129B ALA* 1.3 74.6 - - - +
131B LYS* 1.3 61.6 + - - +
133B LYS* 3.0 25.0 + - + +
134B ASN 3.3 0.2 + - - -
135B TYR* 3.0 45.1 + - + +
137B LEU* 3.8 40.4 - - + +
142B LEU* 4.4 3.6 - - + -
163B LEU* 4.3 29.8 - - + +
165B PHE* 4.1 17.3 - - + -
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ARG 2.9 17.3 + - - +
128B ALA* 3.4 7.6 - - - +
129B ALA 3.3 0.2 - - - -
130B LEU* 1.3 77.6 - - - +
132B LYS* 1.3 56.9 + - + +
134B ASN* 3.0 18.5 + - - -
135B TYR 3.3 13.8 + - - +
9F C 3.5 30.8 + - - +
10F T 3.0 34.1 + - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA* 3.1 25.9 + - - +
129B ALA* 3.6 13.2 - - - +
130B LEU 3.2 0.4 - - - -
131B LYS* 1.3 75.7 - - + +
133B LYS* 1.3 60.8 + - + +
134B ASN* 3.2 2.6 + - - +
8F T 5.7 2.9 - - - -
2H T 5.4 16.2 - - - -
3H A 5.2 20.6 - - - -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA 3.6 10.6 + - - +
130B LEU* 3.0 13.8 + - + +
132B LYS* 1.3 78.3 - - + +
134B ASN* 1.3 69.2 + - - +
135B TYR* 3.1 29.3 - - + -
144B LYS* 3.8 6.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il